The typhoon has since been weakened, but I have a question: is air service in Japan shut down similar to how our airports in the US shut down when a typhoon approaches? I'm recalling SQ 006 crashing in a typhoon, do airlines still operate in typhoons?

First - SQ 006 crashed partially due to bad visibility from rains from a typhoon. That aircraft was not operating 'in a typhoon' but in the safe aircraft operations area on the outskirts of a typhoon. The typhoon center was 360 km south of the airport at the time of the accident.

A routine METAR 16 minutes before the crash had winds from 020 at 36 kts with gusts to 56 kts and 600 meters visibility in heavy rain. An additional METAR 3 minutes after the crash had winds from 020 at 30 kts with gusts to 61 kts and 600 meters visibility in heavy rain.

Certainly not what anyone would call nice weather - but well within the capability of the aircraft to operate safely.

Flightaware shows Narita and Haneda operating normally.

It looks like the typhoon is well past Tokyo by Sunday evening US time - having come ashore about 12-14 hours earlier - say early morning US time.

Yes, air service was affected in Japan. It affected me at HNL. On Sept. 29, JAL, ANA, and HA delayed returning flights to Japan. On Sept. 30, we have had arrival delays from Japan. JAL and ANA each still have a NRT-HNL flight that is not due to arrive until 21:30 tonight (Sept. 30 in HNL). JAL even delayed JL84, NGO-HNL, to leave NGO at 19:00 on Oct. 1.

It wasn't brought down by the typhoon. SQ006 crashed as it took off from a closed runway and hit the excavators and bulldozer. But then, I guess you can blame the poor visibility at that time and they didn't realize they entered the wrong runway and there were construction equipments blocking the closed runway.

Quoting TreeHillRavens (Reply 3):But then, I guess you can blame the poor visibility at that time and they didn't realize they entered the wrong runway and there were construction equipments blocking the closed runway.

That's my point though, even outside of the center of circulation, there are still severe visability issues which could adversely affect safe travel.
Good to see things operating as normal now, with little damage being reported at NRT and HND.

Okinawa was slammed hard. A Navy guy showed a video on Youtube of a car literally being tumbled around by the winds.